Contacts of the helix formed by residues 46 - 55 (chain W) in PDB entry 3MQT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 46 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53J PHE* 5.4 0.7 - - + -
56J ILE* 3.4 49.1 - - + -
57J GLU 5.8 0.2 - - - +
59J GLU* 4.1 9.8 - - - +
63J LEU* 4.6 4.0 - - + -
92J ILE* 3.7 24.2 - - + -
45W GLY* 1.3 78.4 - - - +
47W PRO* 1.3 74.4 - - + +
48W GLU 3.4 1.8 - - - -
49W CYS* 3.1 9.3 + - + +
50W MET* 2.9 31.3 + - + +
97W LEU* 4.4 7.4 - - + -
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Residues in contact with PRO 47 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J GLU* 4.1 4.9 - - - +
14W PRO* 3.8 19.9 - - + +
15W VAL 4.5 2.2 - - - +
16W ASN* 4.3 11.0 - - + +
25W ASN* 3.7 35.0 - - + +
26W THR 3.6 25.6 - - - +
27W VAL* 3.4 16.3 - - + +
45W GLY 3.1 9.0 - - - +
46W PRO* 1.3 84.1 - - + +
48W GLU* 1.3 59.2 + - + +
50W MET* 3.2 3.5 + - - +
51W LYS* 3.0 27.9 + - - +
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Residues in contact with GLU 48 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J ALA* 4.8 4.8 - - + +
56J ILE* 6.5 0.2 - - + -
14W PRO* 3.6 27.2 - - + +
16W ASN* 6.1 2.7 - - - +
46W PRO 3.4 0.4 - - - -
47W PRO* 1.3 77.8 - - + +
49W CYS* 1.3 62.6 + - - +
51W LYS* 3.4 19.5 + - - +
52W ALA* 3.0 21.5 + - - +
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Residues in contact with CYS 49 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J CYS* 4.1 14.1 - - - -
52J ALA* 4.1 10.2 + - + +
53J PHE* 3.7 45.3 - - - +
56J ILE* 4.1 10.8 - - + +
97J LEU* 5.4 0.4 - - - -
46W PRO* 3.1 24.9 + - + +
48W GLU* 1.3 78.8 - - - +
50W MET* 1.3 56.1 + - - +
52W ALA* 3.1 4.0 + - - +
53W PHE* 3.0 26.5 + - - +
97W LEU* 4.4 14.6 - - - -
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Residues in contact with MET 50 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W PHE* 3.5 18.1 - - + -
27W VAL* 3.9 13.9 - - + -
43W ALA* 4.6 3.6 - - + -
44W ASP 3.6 20.2 - - - +
45W GLY* 3.6 19.5 - - - +
46W PRO* 2.9 21.9 + - - +
47W PRO 3.7 4.3 - - - +
49W CYS* 1.3 73.5 - - - +
51W LYS* 1.3 65.6 + - - +
53W PHE* 3.2 5.9 + - + +
54W SER 3.1 18.0 + - - -
97W LEU* 3.7 43.5 - - + +
100W PHE* 3.9 4.9 - - + -
101W ALA* 3.9 33.7 - - + +
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Residues in contact with LYS 51 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W PHE* 3.4 28.3 - - + +
14W PRO* 3.7 20.2 - - + -
27W VAL* 5.2 0.6 - - + +
47W PRO 3.0 13.0 + - - +
48W GLU* 3.5 24.7 - - - +
49W CYS 3.3 0.2 - - - -
50W MET* 1.3 75.2 - - - +
52W ALA* 1.3 62.9 + - - +
54W SER* 2.6 25.5 + - - +
55W GLU* 3.1 42.3 + - - +
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Residues in contact with ALA 52 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J GLU* 4.9 2.9 - - + +
49J CYS* 4.1 15.2 - - - +
52J ALA* 4.1 20.2 - - + -
48W GLU 3.0 13.9 + - - +
49W CYS 3.1 8.9 + - - +
51W LYS* 1.3 75.7 - - - +
53W PHE* 1.3 62.8 + - - +
55W GLU* 3.1 16.6 + - - -
56W ILE* 3.3 16.7 + - - +
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Residues in contact with PHE 53 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J PRO* 5.5 0.4 - - + -
49J CYS* 3.7 14.6 - - - -
97J LEU* 3.9 22.0 - - + -
49W CYS 3.0 13.2 + - - +
50W MET* 3.6 11.7 - - + +
51W LYS 3.2 0.4 - - - -
52W ALA* 1.3 76.2 - - - +
54W SER* 1.3 65.1 + - - +
55W GLU 3.2 1.2 + - - -
56W ILE* 3.3 24.7 - - + +
66W ILE* 4.4 18.4 + - + +
89W THR* 5.2 7.4 - - + -
92W ILE* 3.9 35.4 - - + -
97W LEU* 3.9 19.3 - - + -
98W GLY* 3.5 26.5 - - - -
101W ALA* 3.6 31.4 - - + -
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Residues in contact with SER 54 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W PHE* 3.5 53.3 - - - +
50W MET 3.1 3.4 + - - -
51W LYS* 2.6 18.3 + - - -
53W PHE* 1.3 77.4 - - - +
55W GLU* 1.3 64.4 + - - +
56W ILE 3.6 0.4 - - - -
65W ASN* 2.9 17.3 + - - -
66W ILE* 4.2 11.7 - - - -
67W LYS* 3.2 25.3 + - - +
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Residues in contact with GLU 55 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12W PHE 5.0 2.6 + - - +
51W LYS* 3.1 54.8 + - - +
52W ALA* 3.1 10.7 + - - +
53W PHE 3.1 1.0 - - - -
54W SER* 1.3 86.7 + - - +
56W ILE* 1.3 62.7 + - - +
57W GLU* 5.7 0.5 - - - +
65W ASN* 3.6 4.0 - - - +
67W LYS* 3.9 14.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il